This is what I have done so far:
- Convert Bval and Bvec to B-matrix.
- Convert DWI .nii file to readable .mat file. (changed the permute gradient components [y x z] and the flip sign of gradient components (x y -z) so that the DEC map looks normal). Matriz size 128 128 67. Number of DWI images (32).
- Flip dimensions of T1-weighted image (Default settings: permute dimensions: 1 2 3 & Flip dimensions: 0 0 0)
- Mask background of T1-weighted image (Kernel size: 3 Threshold: 0.02)
- Crop size
- Activated EPI correction in settings (“Yes- to do the EPI correction (non rigid)” and chosen masked the T1w image.
- More settings: Type of registration: “FA” Deformation axes: “1 0 0”
I have I question. Do the T1 and DWI have to have the same matrix?
Thank you in advance!